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The last 2 columns of wgbstools convert -L command apparently are CpG start index and CpG end index. Are they 0-based or 1-based? They don't seem to be consistent with output of wgbstools convert -r. Example:
$ cat s.bed
chr1 185606 185761
$$ bedtools getfasta -fi reference.fa -bed s.bed
>chr1:185606-185761
GACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGTCGATCCCTGACCCAGCACCAGGCACTGATGAGACAGCGGCGGTTTGAGGAGCCACCTCCCAGCCACCTCG
$wgbstools convert -r chr1:185607-185761 # here I assume `-r` option takes 1-based start and end
chr1:185607-185761 - 155bp, 5CpGs: 2175-2180
$wgbstools convert -L s.bed
chr1 185606 185761 2174 2180
2180-2174=6
2180-2174+1=7
So no matter how I calculate it, I cannot arrive at 5.
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